Hydrodynamics in a shallow seasonally low-inflow estuary following eelgrass collapse

Hydrodynamics play a critical role in mediating biological and ecological processes and can have major impacts on the distribution of habitat-forming species. Low-inflow estuaries are widespread in arid regions and during the dry season in Mediterranean climates. There is a growing need to evaluate dynamics and exchange processes in these systems and the resultant ecological linkages. We investigate the role that hydrodynamics play in shaping environmental gradients in a short and seasonally low-inflow estuary located along the central California coast. Since 2007, eelgrass meadows in Morro Bay have declined by more than 90%, representing the collapse of the major biogenic habitat. Despite the large-scale decline, eelgrass beds near the mouth of the bay remain resilient, suggesting that conditions in certain areas of the bay might allow or impede eelgrass retention and recovery. Oceanographic moorings were deployed throughout the bay during the summer dry season to assess spatial differences in environmental conditions and hydrodynamics across gradients in eelgrass survival. Relative to the mouth of the bay, the back bay water mass was significantly warmer (hyperthermal), more saline (hypersaline), less oxygenated, and more turbid, with longer flushing times, all of which have been identified as significant stressors on seagrasses. Moreover, there is weak exchange between the mouth and the back bay that effectively decouples the two water masses during most periods. Though the causes of the decline are not clear, gradients in environmental conditions driven by bay hydrodynamics appear to be preventing eelgrass recovery and restoration attempts in the back bay and keeping this region in an alternative state dominated by unvegetated intertidal mudflats. Ecosystems in low-inflow estuaries may be especially prone to ecological regime shifts or collapse and may require precautionary monitoring and management. This system and the dramatic ecological change that it has experienced, demonstrate the critical role that hydrodynamics play in ecosystem health and habitat suitability